Confusion and Empathy
by SherlockMuser
Summary: This is my first ever fic. Review please! Definite John/Sherlock later on. John and Sarah end their relationship but Sherlock can't deduce why. Or how he feels. And John realises something. I own nothing apart from the mac I type on. Rating may go up. :
1. Chapter 1

**A/N**

**Okay, so this is my first fanfic. Ever. So please review it, I'd love to know what you all think.**

**This wasn't intended to be a one-shot, but if you all hate it, I'll stop there. If anybody likes it, I'll try to get the next chapter up as soon as possible :)**

**Enjoy, hopefully! No warnings in this chapter, but be warned there WILL be later on. If it gets that far xD**

-Sherlock's POV-

"Who was that?" Sherlock asked as John put down his phone. It was obvious, but he wanted to prove himself right. He knew it was that girl he spends an awful lot of time with… He just couldn't quite remember her name.

"Sarah." He replied

Ah, of course. The dull name matches the dull personality.

"What did she want?" Sherlock's voice sounded bored, even to himself. He could tell that she wanted to see him. Sooner rather than later, judging by John's growing look of frustration at being asked pointless questions and therefore having his time wasted.

Wait. John thought that Sherlock was wasting his time. That made Sherlock angry for reasons he wasn't quite sure of. He swung his legs off the sofa so he was sitting instead of lying down.

"I know that you already know, Sherlock. I'm not an idiot."

"Really?"

"Piss off. Anyway, I'm off out. I'll be back before 11."

Sherlock glanced at his watch. John had 2 hours, 13 minutes and 47 seconds. He sighed as he looked at the empty space on the mantelpiece where his skull should be. Damn Mrs. Hudson. That reminded him.

"Get some teabags while you're out, John!"

"Get them yourself," Sherlock heard John mutter just before he slammed the door.

"How rude." He said to himself, a frown on his face. He really did want some tea and they had none left. "Mrs Hudson?" He waited for a reply from downstairs.  
"Yes, Sherlock dear?"

"I'll be needing some teabags. Within the next minute or so if possible."

"Just this once. I'm your landlady, not your housekeeper you know, Sherlock."

Sherlock chuckled, and was greeted by Mrs. Hudson in 32 seconds. Very efficient, he thought. He thanked her, and just as she was walking down the stairs;

"Mrs Hudson?"

"Mmm?"

"What have you done with my skull?"

"I haven't the slightest idea what you're talking about, dear."

The cheek of her, Sherlock thought. He now had 2 hours, 11 minutes and 22 seconds alone with nobody but himself to talk to. At least he had tea now. He stood up and grabbed the teabags Mrs. Hudson had left on his coffee table. He put one of them in a mug and poured some water into the kettle. He flicked it on and opened the fridge, and to be honest, he was quite surprised that John had bought some more milk. Shame about not remembering the teabags though. Ah, well. Mrs. Hudson's would do for now.

He finished making his tea and sat back down on the sofa, sipping his drink while contemplating what to do next. There were no cases to solve, even though he had informed Lestrade to alert him as soon as anything interesting came up. He had no experiments he currently wanted to perform, and anyway, he was still being closely watched from that incident with the eyeballs in the microwave. He put down his mug and found himself wishing that he had someone to talk to. He had no skull and no John, and he needed someone to listen to him thinking aloud.

He fetched his beloved violin from his room and decided to turn his thoughts into music. He wasn't sure how it worked, it just happened from all that he could deduce. This evening, he was quite surprised to hear that the tunes he was plucking out were rather melancholy. This confused him, as however bored he may be right now, he wasn't at all sad, was he? He certainly had no reason to be sad. He and John had fun during the daytime, whether it be mocking Anderson or shouting at crappy telly. John went out most evenings, leaving him with the alone time he craved so much… His brain paused at this. He didn't quite seem to be enjoying his alone time as much as usual. Probably because Mrs. Hudson had his skull. Yes, that was it. He missed his skull. He smiled slightly at this simple conclusion, but couldn't help thinking that there was something more.

Not that he could dwell on it much, as his thoughts were interrupted by John coming back. That was odd, he was home 1 hour, 36 minutes and 53 seconds earlier than he said he would be. He was out for less than half the time he had estimated. Therefore, something had happened to cut the date short. He would have asked what, but then he thought that it might have been insensitive.

Hang on. He was Sherlock Holmes. Since when was he bothered by sensitivity? Since now, apparently.

"John?"

"Let me get in the door for Christ's sake."

Sherlock could hear a hint of something unfamiliar in his voice… Sadness, perhaps. Embarrassment, a bit of remorse, maybe even some shock. He didn't, however, get the anger he had been expecting. He came to the conclusion that Sarah had dumped him. But he wasn't at all angry. That changed things. From what he had observed, people usually got angry when someone they cared about cast them aside. So John must have dumped her. Well that was unexpected.

John sat down on the armchair that was now his, and put his head in his hands. This shocked Sherlock; he wasn't used to seeing his flatmate like that, and wasn't sure how to handle it. However much he wanted to be sensitive, he wasn't sure he knew how.

"Um, John? Are you okay?" He asked as soothingly as was possible for him.

"I'm fine," His voice was muffled slightly from his hands. "Did you get teabags?" He said, looking up.

Sherlock pointed over to the ones that Mrs. Hudson had given him earlier.

John stood up, but then so did Sherlock, who made his way over to the kitchen faster than John could. He decided the friendly gesture of making his flatmate tea, which he hardly ever did, was going to be Sherlock's own little way of showing that he didn't want to pry. And from the grateful look on John's face, he accepted it.

As Sherlock was making yet more tea, he noticed a flicker of a smile trying to break through on his lips. It was followed by a frown. What kind of an insensitive bastard would smile when his best friend had just broken up with his girlfriend? Then he remembered.

He would.

He winced slightly at this thought. That couldn't be the reason he was smiling, could it? That John and Sarah had split up? No, Sherlock thought. It was merely because he was happy to have someone to talk to at a time when he was so… Bored.

Yet again, he felt like there was more to it than that. He wondered what it was, but however much he deduced about himself, he just couldn't find any reason at all. But he was sure there was. Even though this frustrated him a great deal, he decided to leave it be, because the only reason he wouldn't be able to find out was if his brain was trying to hide something from him. And it did far too much of a good job of it for his liking.

He walked over and handed John his tea.

"Thanks." The smaller man said quietly, and then sighed before putting the mug to his mouth.

Sherlock sat down, looking at John intently, trying to deduce what sparked the break-up. And for the life of him, he didn't know. His eyes narrowed slightly and a frown formed on his face. They had seemed perfectly happy together. John definitely liked her a lot more than he had ever let on. So why would he dump her? He was deep in thought, and hadn't noticed John looking at him with one of his eyebrows raised.

"So, how much have you managed to deduce so far, Sherlock?" His voice sounded worn out and slightly spiteful. He could tell that John didn't want to talk about it, so Sherlock shook his head.

"It doesn't matter," He said, but then realised that this might sound like he didn't care. And he did. However weird that may be for Sherlock, he had to admit it to himself. He didn't like seeing John upset. "I mean, it's none of my business, is it?"

John stared down at the carpet. Something clicked in Sherlock.

"It's to do with me, isn't it?" He asked, scared that John hated him for… Whatever it was he had done. He saw John shut his eyes and lift up his head.

"Yes... Well, not directly, at least."  
What? Really, what? John was being far too cryptic.

"Then why did you break up with her?"

John frowned at him. "You're losing your touch. She ended it with me."  
Damn. Wasn't expecting that.

"What? Why? Aren't you supposed to be angry about this?"

John laughed gently. "No, not at all. I completely understand why she did it. In fact, I completely agreed with her reasons. I don't blame her at all."  
"Then why are you so upset?" Sherlock was extremely confused. He was still a very long way off understanding the emotions and reasoning of normal people.

"It just… Brought home a few things that I really wasn't really prepared to admit to myself. That's all. I'm not upset, I'm just," He sighed. Again. "Not really sure how I feel right now. Or how I should feel, for that matter."

Sherlock's veil of confusion lifted with the realisation that he could actually relate to that. For the first time in his life, Sherlock was able to relate to a person. This gave him a strange feel of contentedness. But he was still curious.

"So, why does Sarah feel that she has to break up with you because of me?" And the fact that John agreed with her on this matter was more than slightly intriguing.

"It doesn't matter," came John's completely unsatisfying response. "And if you don't mind, I think I want to get to bed now."

Sherlock did mind. He minded a great deal, actually. But he wasn't going to press John for answers right now. Maybe he'd feel better in the morning. He watched John walk up the stairs, and heard his bedroom door open and shut. He picked up his violin again, and this time the tune was different. It still had it's underlying melancholy, but it also had some happier tunes; It was almost as if it were encouraging him, saying, "I understand."

Well at least someone did.

**So... What did you think? REVIEW TIME! Tell me what was good, what was bad, whether I should carry on, etc and you shall receive a limited edition hug from SherlockMuser. Call me Mary if you want xD**

**Thanks for taking your time for reading this, I really appreciate it :)**


	2. Realisation

**A/N Okay. So I thought this was quite efficient xD It's a bit shorter than the 1st chapter, but I hope you won't mind :)**

**Thanks to everyone who reviewed my first chapter - You were all unbelievably encouraging and I love you all :D**

**In all honesty, I don't particularly like this chapter. John relives the breakup and then has a bit of a breakdown. Not because of the breakup, but because of what the breakup made him realise. I don't like writing in John's POV and I think it's all a bit overly emotional but you can judge for yourselves. Next chapter won't be this emotional, so please read anyway even if it's not your cup of tea xD**

**(Please bear in mind I have literally only just finished, and it's 5:40 in the morning and I am _extremely _tired. Please forgive any stupid mistakes.)**

-John's POV-

John shut his door and laid his forehead on it, wondering what to do next. He wasn't at all tired, but neither was he prepared to explain to Sherlock why he and Sarah had broken up. He still couldn't quite believe it himself, but remembering his and Sarah's earlier conversation he realised that it was the only rational explanation for everything he felt towards the strange man.

"_John, I love you." That was a shock in itself. Never had either of them told the other that. John wasn't sure how to react; he didn't love Sarah, but he cared for her too much to break her heart by saying so. He was in a slight panic about what he should do or say, when thankfully she saved him the embarrassment._

"_But I know you don't feel the same. Now if I didn't know better, I'd say that we could work at this relationship. But I do know better. And as much as it pains me to say it, I think you could be a lot happier with someone else. In fact, I think you _are_ a lot happier with someone else…"_

_John was dumbstruck. The only person he was suitably happy with apart from Sarah was Sherlock. She couldn't mean- He cut off his own thought. No. Of course not. John wasn't gay. He opened his mouth to tell Sarah this, but was beaten to it._

"_I know what you're thinking, and John, I know it's hard to accept. But if you remember all the conversations we've had, the only thing you ever really talked about was Sherlock. And from what you've said, he sounds fantastic, John, just perfect for you,"_

_John was sure she was still talking, but he couldn't pay any more attention. He was sure his eyes had glazed over, and he felt slightly nauseous. In his head he went through everything Sarah had just said about him, finely picking through all of his own thoughts in relation to her observations, right down to the last tiny details. He couldn't help himself, he thought about Sherlock. He was wondering if that was how his mind worked all the time, thoroughly analysing each supposedly insignificant thing to hopefully reach a solid conclusion. It was bloody tiring, that was for sure._

_He slowly realised as his trail of thought inevitably ended up with Sherlock in it as they always did, that Sarah was right. It was a shock to his system, but it was a long overdue one. He looked up at his soon-to-be-if-not-already-ex-girlfriend and saw her looking back with a startlingly huge amount of comfort on her face. She took his hand and gave it a gentle squeeze that he returned: From her it was a squeeze of understanding, from him a squeeze of apology. John let go of her hand and put both of his on her face, and hadn't realised until then that she was crying. He wiped away her silent tears with his thumbs, and leaned in to give her a tender kiss._

"_I'm sorry." And he was. He was so, so sorry._

"_It's okay love. Now you go home and talk to Sherlock."  
"I'll miss you. You were brilliant," He whispered. "Bye, Sarah."  
"Bye, John."  
And with one last gentle stroke of her cheek he left. He didn't turn back, afraid that if he did, he'd have to go running back to her and tell her that she was wrong and he never wanted to leave her, that Sherlock was his friend and nothing more, and never _would _be anything more._

_But they were lies. And he couldn't lie to her. Not after how truthful she had been with him._

John stood up straight, looking in the mirror to see the red circle on his forehead where he'd been leaning on his door for so long. He giggled silently to himself, needing a bit of a laugh after everything he'd been through this evening, and sat down on his bed. He could hear Sherlock playing his violin downstairs, so he closed his eyes and laid on his bed, just listening to it for a few minutes. The sound had so much yearning in it, and something about that made John want to go down there and give the man a hug. He wouldn't, of course. Sherlock was a sociopath and would freak out at that, no doubt.

John was just thinking that maybe he was tired after all, and was close to falling asleep when the music suddenly stopped. That was annoying. Without the music, John had nothing to listen to but his own thoughts, and he'd had enough of them for today, thank you very much. He was about to go and tell Sherlock to keep playing; he was enjoying it for once, when he heard a knock at his door.

He got up and opened it, and saw Sherlock on the other side. He hasn't brought his violin, John thought. Wait, why would Sherlock bring his violin? Why would Sherlock be in his room at all? He squeezed his eyes shut for a moment and then opened them again. Still there. And looking somewhat confused.

"John," the taller man inquired, "Why is your forehead pink?"

John smiled and shook his head.

"I thought you were meant to be able to work that kind of thing out in the blink of an eye. Why are you here anyway?"

"Thought you might need some company. You didn't look very tired when you left the living room. And you didn't go to the bathroom first to brush your teeth either, so you couldn't have gone to sleep."

John gestured for Sherlock to sit down. He sat on the edge of John's bed and John closed the door, sitting down next to him. They sat in silence for a little while. Not awkward silence, but a silence that said they were completely comfortable with each other's company. After a while John found himself looking at the man sitting beside him. He looked at his dark curly hair that was rather messy, suggesting that Sherlock had been running his hands through it. He then looked at his eyes, his pale grey eyes. His pale grey eyes that were looking right back at him.

Shit.

John's breathing became uneven and his heart rate rose considerably. He swallowed what little saliva there was in his mouth, and he was still looking into those eyes. He couldn't look away for even a fraction of a second, he couldn't even blink. His eyes started stinging after a while and he realised, blushing heavily, that he was crying. He immediately looked away, and wiped his face clear of moisture. He didn't know why he was crying, but he couldn't stop it. As soon as he dried his face, more came trickling down. Just as he was about to stand up and leave because of pure shame, he felt a hand on his shoulder. It was a soothing hand, and it gently rubbed his shoulder until the tears stopped. As a doctor, he was sure that the shoulder wasn't in any way connected to the tear ducts, but somehow this repeated motion had ended his crying.

He turned round to look at Sherlock, and tears formed in his eyes all over again. What was wrong with him? He was contemplating what he should do about it, when Sherlock removed his hand from his shoulder, and put his arm around John's waist, pulling him closer until his head was on Sherlock's chest. He could hear the gentle beating of his heart and feel the steady rise and fall of his breathing. He could feel Sherlock caressing him as he rocked him like a baby. John let his tears spill freely onto Sherlock's shirt until he fell into a deep sleep.

**A/N Sooo... a bit cringey? Too much emotion for a soldier who served in Afghanistan? You tell me.**

**Review please, you don't know how much it means to me :)**


	3. Conclusion

**A/N Okay, so this is going to be the last chapter because it just seemed right to end there, and it wasn't really going anywhere else.**

**Thank you so much everyone who reviewed, favourited, and put my story on alert, it's a huuuge encouragement :)**

**Warning: There are a few sexual themes, but nothing much because I wanted to keep it within T rating. Trust me I was tempted. Oh so tempted. But it was the right place to stop and I would have gone on forever with it if I hadn't stopped there, before it got REALLY hot.**

**So, enjoy :D**

-Sherlock's POV-

Sherlock sat there, his flatmate asleep on his chest, still stroking and rocking him. He'd been there so long he'd lost track of time, and with all due respect to his friend who had just had a breakdown, he was bored.

He adjusted slightly to get his mobile phone out of his pocket, and decided to check BBC news for the unlikely event of anything interesting having occurred. Nothing. He sighed, wondering what he could do now. Before he had to make up his mind, his phone vibrated, with one new text. He looked at who sent it. Mycroft. Typical. He groaned inwardly but opened it anyway.

**Is Dr. Watson quite all right? He seemed rather upset earlier.**

**MH**

Stupid Mycroft, spying on them when none of it was any of his business. He wished his older brother would leave them alone.

**John is fine. Bugger off and stop spying on my flatmate.**

**SH**

It wasn't technically a lie. John was fine, for now. When he woke up, though, it would be a whole other matter. Sherlock looked at John sleeping on him. He seemed so peaceful, which was unlike him as he usually had nightmares. John didn't think Sherlock knew, but there were always the telltale signs of the circles around his eyes in the morning, and the quiet whimpers at night. Sherlock thought about doing this more often; the nightmares worried him because he knew John was afraid. His friend would never let him though; he'd hate him after being brought to tears by him. Even if John didn't hate Sherlock, he sure as hell would be embarrassed to be around him. His phone vibrated again.

**It's for his and your own good. You'll thank me for it at one point.**

**MH**

Hah. That'd be the day. Sherlock snorted.

**No I won't.**

**SH**

He threw his phone down on the bed, and felt John move. He looked down and John's eyes flickered open.

"Sherlock?" He asked, still groggy from sleep.

"Hi," Sherlock said gently, unsure of himself. "Did you sleep well?"

"Surprisingly so."  
"Do want anything? Tea? Coffee?"  
"Coffee would be nice."  
"Well go make some." Sherlock said in a humorous tone of voice, trying to get back to normal as soon as he could. John chuckled, and lifted his head from Sherlock's chest. He stood up and walked down the stairs. No signs of dislike or awkwardness or embarrassment or shame, thank God. Sherlock went to the bathroom and had a shower.

When Sherlock emerged from the bathroom with a towel round his waist, John was sitting down, watching television and drinking his coffee. Just as Sherlock was about to make his way to his bedroom to get dressed, John called him.

"Sherlock," The consulting detective turned round to face John.

He was well aware that his chest was bare and moist, and his hair was sticking to his scalp and face, but he didn't ever think that he'd render John speechless. The doctor was sat there just staring at Sherlock. It was like last night, he thought, when he'd been looking into John's eyes trying to deduce whatever the problem was. Oh God, he thought. Please don't cry again. He couldn't deal with more tears, so he quickly made his exit.

"I'm just going to get dressed John. I'll be right back"

Sherlock really drew out the process of getting dressed, as he needed time to think. What was causing John to cry? He had said that he wasn't upset with or angry at Sarah for breaking up with him, and Sherlock believed him. So it wasn't that. He had said that he agreed with her reasons, even. So it must be these reasons that were causing him so much upset. And it was to do with him. Sherlock didn't like this, but it gave him a sense of responsibility. He had to know what he was doing to upset John.

He was dressed now, but decided to give it one last think over. When he was sitting next to John on his bed, John was looking at him with a kind of look nobody had ever given him before. So he didn't know what it was. But when they had looked into each other's eyes, John's breathing had gone awry and his heart started beating so loud that Sherlock could hear it. He ran these things through in his mind, and-

Oh.

_Oh._

He knew those signs. It was like that silly girl at St. Bart's, Molly Hooper. But this was different. John was his friend. He and John cared about each other, but it was never anything more than that. Because John was straight, wasn't he? Sherlock may have a preference for the male body, but John was strictly off limits, he was Sarah's. And now… Now all those feelings of there being something more in Sherlock's emotions made sense. John liked him. As more than a friend. And now he knew that, his brain decided that there was no risk in telling him that he felt the same way because there was no way he could get hurt, or at least, not that Sherlock knew of. He was happy, oh so happy.

He opened his door quietly, and crept over to where John was seated. He crouched down beside him, and whispered into his ear.

"John," Wow. He had no idea his voice could be so… Seductive.

John whirled round, and his face was barely a centimetre away from Sherlock's. Sherlock could taste his warm, coffee-flavoured breath and shut his eyes for a moment, opening them to see John's unbelieving face.

"mmng?" John's incomprehensible response got him a chuckle from Sherlock.

"I know, John." He whispered. He gently took his best friend's face in his hands and leant in closer, barely breathing his next words. "I know why you and Sarah broke up."

And with that, he closed the distance between their lips. They were still for a second, but then Sherlock prised open John's lips and started a long, tender kiss. Sherlock was drowning in emotions as John moved his hands to his mop of still damp hair, he was being asphyxiated by all those long buried feelings. Literally.

He pulled away, gasping for air, a grin on his face that was matched by John's. He went straight back in, kissing John's neck, nibbling his earlobe, listening to his moans.

"Sherlock," John managed to get out.

Sherlock made a noise to show that he was listening, but he didn't stop, he'd never stop if it wasn't absolutely necessary. The feeling of John's neck, his ears, his lips, on Sherlock's mouth, was extraordinarily addictive, as was hearing how much John was enjoying it through his more than frequent gasps and moans.

"You don't have to do this. For me, to make me happy. If it's not what you want."

This made Sherlock stop. John thought that he didn't want this. He moved his eyes up to John's, which looked like they regretted making him stop, and raised an eyebrow. This made John shiver, so Sherlock smiled. He didn't deliberately change his voice at all, but it came out somewhere between a growl and a purr.

"John Watson, do you know how long I have been waiting for this?"

John didn't reply, but Sherlock was pleased about this because if John was busy talking, he couldn't have pulled Sherlock's mouth back up to his. This kiss was so passionate and fiery that Sherlock was sure that it would lead to much, much more. He started thinking about what he wanted to do to John, and he felt arousal flooding through his body. Apparently John felt the same way, as he was pulling Sherlock onto the sofa. Sherlock positioned himself on top of John and started pushing down on him and moving against him, which felt so unbelievably brilliant he started moaning himself. He was about to unzip John's jeans, when he heard the door open and looked round to see Mrs. Hudson standing at the door, mouth agape and a blush creeping up her neck.

He was expecting her to leave straight away, but before she did, a grin appeared on her face, and she said with pride " I knew it! I bloody knew it!"

Sherlock laughed, the movement of it making John moan before he realised Mrs. Hudson was still there, and John went bright red, causing Sherlock to laugh even more.

"I'll leave you boys to it, eh?" She said with a wink, and firmly shut the door on her way out.

"Now… Where was I before we were so rudely interrupted?" Sherlock asked rhetorically, and got back to his job of taking John's jeans off.

**A/N So that's the end! I'm sorry I deprived you of a full on sex scene, but I'm sure there'll be more stories to come... No pun intended xD**

** Did you like it? Review please, I want to know what you thought of the story as a whole, how I can improve and what I should do next.**

**Thanks go to:  
Everyone who used up valuable minutes of their time to read something that I wrote... (INCLUDING YOU!) I still can't believe that people from across the globe are reading my story.**

**Other authors who have written stories on here that I will never be able to live up to in a million years, for keeping me sane and giving me inspiration.**

**And of course, Sir Arthur Conan Doyle for his invention of these amazing characters, and the BBC for bringing them to the 21st Century. And Benedict Cumberbatch and Martin Freeman for portraying these characters ridiculously well.**

**THANKS OVER! REVIEW NOW! GOGOGO!**


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